A nomenclature system for labeling cyclic peptide fragments

A nomenclature system for labeling fragment ions of cyclic peptides is prop osed. A fragment ion is labeled with a four-part descriptor of the general formula x(nJZ), where x is the designation for the ion (e.g., lower case a or b, as are used for peptide fragments) and n is the number of amino acid residues in the ion. A b ion is the usual acylium ion or isomeric equivalen t consisting of n amino-acid residues, and this ion may lose carbon monoxid e to form an a ion. The subscripts J and Z are the one-letter (upper-case) codes for the two amino-acid residues connecting the backbone amide or este r bond, J-Z, that can be viewed as broken to form the decomposing Linear io n. The symbol J is for the N-terminal amino-acid residue, and Z is that for the C-terminal amino-acid residue that result from the bond cleavage. The nomenclature system is applicable to a wide range of cyclic peptides, inclu ding depsipeptides, cyclic peptides containing modified or unusual amino ac ids, cyclic peptides bearing a linear peptide moiety, and cyclic peptides t hat are introduced into the gas phase as metal-ion cationized species. (C) 1999 American Society for Mass Spectrometry.